Hi again !
I am glad to hear that you are an experienced user :-)
However, may I still suggest that you post on the Apple Discussions, call Apple or your usual support provider ? Indeed, you really should not experience issues.
Its architecture allows it to be very resistant to faulty third-party applications. However, using such software in your workflow is not recommended either !
Apple always does its absolute best to improve the quality of its products and welcomes your feedback. Would you think that you have located a bug, there are many feedback channels available. Also, would you have some coding experience, you can become an ADC member — membership is free.
For your information, FileVault does not use a proprietary encryption system. More information may be found here : http://www.apple.com/macosx/features/filevault/